new file: a/ANSYS/ANSYS-2023R1-intel-2022a.eb

new file: b/Boost/Boost-1.79.0-intel-compilers-2022.1.0.eb new file: c/CheMPS2/CheMPS2-1.8.12-intel-2022a.eb new file: g/gau2grid/gau2grid-2.0.7-intel-2022a-lmax-5-psi4.eb new file: m/mctc-lib/mctc-lib-0.3.1-GCC-11.2.0.eb new file: m/msgpack/msgpack-1.0.5-GCCcore-11.3.0.eb new file: p/Pint/Pint-0.20.1-GCCcore-11.3.0.eb new file: p/pydantic/pydantic-1.10.6-GCCcore-11.3.0.eb new file: q/qcengine/qcengine-0.24.1-foss-2021b.eb new file: q/qcengine/qcengine-0.24.1-psi4.patch new file: q/qcengine/qcengine-0.26.0-foss-2021b.eb new file: q/qcengine/qcengine-0.26.0-psi4.patch new file: s/simple-dftd3/simple-dftd3-0.7.0-foss-2021b.eb deleted: c/CheMPS2/CheMPS2-1.8.9-intel-2021a.eb
2025-04-04 06:11:36 +01:00 · 2023-03-13 17:11:24 +01:00 · 2023-03-13 17:11:24 +01:00 · 4fbadeb08a
commit 4fbadeb08a
parent 31fd70556d
13 changed files with 422 additions and 5 deletions
--- a/a/ANSYS/ANSYS-2023R1-intel-2022a.eb
+++ b/a/ANSYS/ANSYS-2023R1-intel-2022a.eb
@ -0,0 +1,36 @@
+# IT4Innovations 2023
+# JK
+
+name = 'ANSYS'
+version = '2023R1'
+
+homepage = 'http://www.ansys.com'
+description = """ANSYS simulation software enables organizations to confidently predict
+ how their products will operate in the real world. We believe that every product is
+ a promise of something greater. """
+
+toolchain = {'name': 'intel', 'version': '2022a'}
+
+sources = [
+    {'filename': '%(name)s%(version)s_LINX64_DISK1.iso', 'extract_cmd': '7z x -aos %s'},
+    {'filename': '%(name)s%(version)s_LINX64_DISK2.iso', 'extract_cmd': '7z x -aos %s'},
+    {'filename': '%(name)s%(version)s_LINX64_DISK3.iso', 'extract_cmd': '7z x -aos %s'},
+]
+checksums = [
+    {'ANSYS2023R1_LINX64_DISK1.iso': 'fa3f75c1fa14ae7cf2da56e9912151b4'},
+    {'ANSYS2023R1_LINX64_DISK2.iso': '7cd1c490aeeeede3b8651c747002e4f2'},
+    {'ANSYS2023R1_LINX64_DISK3.iso': '677341a8fd5cb45535115345c7dd55b9'},
+]
+
+dependencies = [
+   ('libGLU', '9.0.2'),
+   ('libnsl', '2.0.0'),
+]
+
+osdependencies = [('p7zip', 'p7zip-plugins')]
+
+import os
+license_server = os.getenv('EB_ANSYS_LICENSE_SERVER', 'license2021.it4i.cz')
+license_server_port = os.getenv('EB_ANSYS_LICENSE_SERVER_PORT', '2325:1055')
+
+moduleclass = 'tools'
--- a/b/Boost/Boost-1.79.0-intel-compilers-2022.1.0.eb
+++ b/b/Boost/Boost-1.79.0-intel-compilers-2022.1.0.eb
@ -0,0 +1,33 @@
+# IT4Innovations 2023
+# JK
+
+name = 'Boost'
+version = '1.79.0'
+
+homepage = 'https://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.12'),
+    ('XZ', '5.2.5'),
+    ('ICU', '71.1'),
+]
+
+#preconfigopts = "sed -i 's/-static//g' tools/build/src/engine/build.sh && "
+# fix test_toolset function so it works correctly for intel-linux toolset;
+# see also https://github.com/boostorg/build/issues/647
+#preconfigopts += "sed -i 's/{TOOLSET}/{B2_TOOLSET}/g' tools/build/src/engine/build.sh && "
+
+# disable MPI, build Boost libraries with tagged layout
+boost_mpi = False
+tagged_layout = True
+
+moduleclass = 'devel'
--- a/c/CheMPS2/CheMPS2-1.8.12-intel-2022a.eb
+++ b/c/CheMPS2/CheMPS2-1.8.12-intel-2022a.eb
@ -4,24 +4,24 @@
 easyblock = 'CMakeMake'

 name = 'CheMPS2'
-version = '1.8.9'
+version = '1.8.12'

 homepage = 'https://github.com/SebWouters/CheMPS2'
 description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the
 density matrix renormalization group (DMRG) for ab initio quantum chemistry."""

-toolchain = {'name': 'intel', 'version': '2021a'}
+toolchain = {'name': 'intel', 'version': '2022a'}

 source_urls = ['https://github.com/SebWouters/CheMPS2/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['ccd4c0d9432759d97690bf37a0333440f93513960c62d1f75842f090406a224d']
+checksums = ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83']

 builddependencies = [
-    ('CMake', '3.20.1'),
+    ('CMake', '3.23.1'),
 ]

 dependencies = [
-    ('HDF5', '1.10.7'),
+    ('HDF5', '1.12.2'),
 ]

 pretestopts = 'export OMP_NUM_THREADS=1 && '
--- a/g/gau2grid/gau2grid-2.0.7-intel-2022a-lmax-5-psi4.eb
+++ b/g/gau2grid/gau2grid-2.0.7-intel-2022a-lmax-5-psi4.eb
@ -0,0 +1,49 @@
+# IT4Innovations 2023
+# JK
+# J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'CMakeMake'
+
+name = 'gau2grid'
+version = '2.0.7'
+local_lmax = 5
+# custom configuration, to be used as dependency for PSI4
+versionsuffix = '-lmax-%s-psi4' % local_lmax
+
+homepage = 'https://github.com/dgasmith/gau2grid'
+description = """A collocation code for computing gaussians on a grid of the form:
+
+out_Lp = x^l y^m z^n \\sum_i coeff_i e^(exponent_i * (|center - p|)^2)
+
+Where the returned matrix dimension are the angular momentum (L) by number of 
+requested points (p)."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/dgasmith/gau2grid/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['66e7205646e1e3685e5dd4eea8281fc92b0b8b45ce97ae24b72a09e15a3fd62f']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+]
+
+# preventing system Python to be picked up:
+local_common_configopts = '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DMAX_AM=%s' % local_lmax
+# perform iterative build to get both static and shared libraries
+configopts = [
+    local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF',
+    local_common_configopts + ' -DBUILD_SHARED_LIBS=ON',
+]
+
+sanity_check_paths = {
+    'files': ['lib/libgg.a', 'lib/libgg.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'chem'
--- a/m/mctc-lib/mctc-lib-0.3.1-GCC-11.2.0.eb
+++ b/m/mctc-lib/mctc-lib-0.3.1-GCC-11.2.0.eb
@ -0,0 +1,24 @@
+easyblock = 'CMakeMake'
+
+name = 'mctc-lib'
+version = '0.3.1'
+
+homepage = 'https://github.com/grimme-lab/mctc-lib'
+description = 'Modular computation tool chain library'
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/grimme-lab/mctc-lib/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083']
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/mctc-convert', 'lib/libmctc-lib.a'],
+    'dirs': ['include/mctc-lib', 'lib/pkgconfig', 'share'],
+}
+
+moduleclass = 'tools'
--- a/m/msgpack/msgpack-1.0.5-GCCcore-11.3.0.eb
+++ b/m/msgpack/msgpack-1.0.5-GCCcore-11.3.0.eb
@ -0,0 +1,30 @@
+# IT4Innovations 2023
+# JK
+
+easyblock = 'PythonPackage'
+
+name = 'msgpack'
+version = '1.0.5'
+
+homepage = 'https://github.com/msgpack/msgpack-python'
+description="""MessagePack is an efficient binary serialization format.
+ It lets you exchange data among multiple languages like JSON. But it's faster and smaller.
+ This package provides CPython bindings for reading and writing MessagePack data."""
+
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'
--- a/p/Pint/Pint-0.20.1-GCCcore-11.3.0.eb
+++ b/p/Pint/Pint-0.20.1-GCCcore-11.3.0.eb
@ -0,0 +1,30 @@
+# IT4Innovations 2023
+# JK
+
+easyblock = 'PythonPackage'
+
+name = 'Pint'
+version = '0.20.1'
+
+homepage = 'https://github.com/hgrecco/pint'
+description = """Pint is a Python package to define, operate and
+manipulate physical quantities: the product of a numerical value and a
+unit of measurement. It allows arithmetic operations between them and
+conversions from and to different units."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'numlib'
--- a/p/pydantic/pydantic-1.10.6-GCCcore-11.3.0.eb
+++ b/p/pydantic/pydantic-1.10.6-GCCcore-11.3.0.eb
@ -0,0 +1,32 @@
+# IT4Innovations 2023
+# JK
+
+easyblock = 'PythonBundle'
+
+name = 'pydantic'
+version = '1.10.6'
+
+homepage = 'https://github.com/samuelcolvin/pydantic'
+description = """Data validation and settings management using Python type hinting."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('typing_extensions', '4.5.0', {
+        'checksums': ['5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb'],
+    }),
+    (name, version, {
+        'checksums': ['cf95adb0d1671fc38d8c43dd921ad5814a735e7d9b4d9e437c088002863854fd'],
+    }),
+]
+
+moduleclass = 'devel'
--- a/q/qcengine/qcengine-0.24.1-foss-2021b.eb
+++ b/q/qcengine/qcengine-0.24.1-foss-2021b.eb
@ -0,0 +1,49 @@
+# J. Sassmannshausen (Imperial College London/UK)
+# Patch: Alexander Grund (TU Dresden/DE)
+
+easyblock = 'PythonBundle'
+
+name = 'qcengine'
+version = '0.24.1'
+
+homepage = 'https://github.com/MolSSI/QCEngine'
+description = """Quantum chemistry program executor and IO standardizer (QCSchema) 
+for quantum chemistry."""
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+builddependencies = [
+    ('pytest', '7.1.3'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('pydantic', '1.10.2'),
+    ('SciPy-bundle', '2021.10'),
+    ('Pint', '0.19.2'),
+    ('simple-dftd3', '0.7.0'),
+    ('PyYAML', '5.4.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('qcelemental', '0.25.0', {
+        'checksums': ['bf5caeeb2044b6056c85e92effc61a21a5ebb1580ccdc165580bb248f8588324'],
+    }),
+    ('py-cpuinfo', '9.0.0', {
+        'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'],
+        'modulename': 'cpuinfo',
+    }),
+    (name, version, {
+        'patches': ['qcengine-0.24.1-psi4.patch'],
+        'checksums': [
+            ('2943866c641dd5f7d73644225bcc9e53155a9423807ddf2706ff679e4f608955'),   # qcengine-0.24.1.tar.gz
+            ('367dc890eef669be1bdbf39b1ab75ad085fe08db24e1eefc95be2069ed4c4662'),   # qcengine-0.24.1-psi4.patch
+        ],
+    }),
+]
+
+sanity_check_commands = ['pytest --pyargs qcengine &> /dev/null']
+
+moduleclass = 'tools'
--- a/q/qcengine/qcengine-0.24.1-psi4.patch
+++ b/q/qcengine/qcengine-0.24.1-psi4.patch
@ -0,0 +1,20 @@
+From: Alexander Grund <Flamefire@users.noreply.github.com>
+Date: Mon, 5 Dec 2022 17:03:50 +0100
+[PATCH] Prepend psiimport path instead of overwriting `$PYTHONPATH`
+When `psi4` binary is found but the Python package is not we should not overwrite the `$PYTHONPATH` before importing `psi4` as that may cause other required packages to be not found anymore. Hence prepend it. See #292
+---
+diff --git a/qcengine-0.24.1.orig/qcengine/programs/psi4.py b/qcengine-0.24.1/qcengine/programs/psi4.py
+index 7dd4d5e..437cdea 100644
+--- a/qcengine-0.24.1.orig/qcengine/programs/psi4.py
+++ b/qcengine-0.24.1/qcengine/programs/psi4.py
+@@ -66,7 +66,9 @@ class Psi4Harness(ProgramHarness):
+         if psiapi and not psithon:
+             psiimport = str(Path(which_import("psi4")).parent.parent)
+             env = os.environ.copy()
+-            env["PYTHONPATH"] = psiimport
+            pythonpath = env.get("PYTHONPATH")
+            # Prepend psiimport to $PYTHONPATH (carefull if it's empty/unset)
+            env["PYTHONPATH"] = os.pathsep.join([psiimport, pythonpath] if pythonpath else [psiimport])
+             with popen(["python", "-c", "import psi4; print(psi4.executable[:-5])"], popen_kwargs={"env": env}) as exc:
+                 exc["proc"].wait(timeout=30)
+             os.environ["PATH"] += os.pathsep + exc["stdout"].split()[-1]
--- a/q/qcengine/qcengine-0.26.0-foss-2021b.eb
+++ b/q/qcengine/qcengine-0.26.0-foss-2021b.eb
@ -0,0 +1,51 @@
+# J. Sassmannshausen (Imperial College London/UK)
+# Patch: Alexander Grund (TU Dresden/DE)
+
+easyblock = 'PythonBundle'
+
+name = 'qcengine'
+version = '0.26.0'
+
+homepage = 'https://github.com/MolSSI/QCEngine'
+description = """Quantum chemistry program executor and IO standardizer (QCSchema) 
+for quantum chemistry."""
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+builddependencies = [
+    ('pytest', '7.1.3'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('pydantic', '1.10.2'),
+    ('SciPy-bundle', '2021.10'),
+    ('Pint', '0.19.2'),
+    ('simple-dftd3', '0.7.0'),
+    ('PyYAML', '5.4.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('qcelemental', '0.25.1', {
+        'checksums': ['e3e0e53fe047d14756718441040a5d737135f0bdb33efb1d63a1935b95821a74'],
+    }),
+    ('py-cpuinfo', '9.0.0', {
+        'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'],
+        'modulename': 'cpuinfo',
+    }),
+    (name, version, {
+        'patches': ['qcengine-0.26.0-psi4.patch'],
+        'checksums': [
+            ('8c10377b11ffab311a2997ae9af80a0f4b4a9c3a6d65d96fd4aca4c941ecf018'),   # qcengine-0.26.0.tar.gz
+            ('ffb51c474eae27777c43ddef264234c1dec4ad7a455cc8ba5051fecbda772f3f'),   # qcengine-0.26.0-psi4.patch
+        ],
+
+
+
+    }),
+]
+
+sanity_check_commands = ['pytest --pyargs qcengine &> /dev/null']
+
+moduleclass = 'tools'
--- a/q/qcengine/qcengine-0.26.0-psi4.patch
+++ b/q/qcengine/qcengine-0.26.0-psi4.patch
@ -0,0 +1,20 @@
+From: Alexander Grund <Flamefire@users.noreply.github.com>
+Date: Mon, 5 Dec 2022 17:03:50 +0100
+[PATCH] Prepend psiimport path instead of overwriting `$PYTHONPATH`
+When `psi4` binary is found but the Python package is not we should not overwrite the `$PYTHONPATH` before importing `psi4` as that may cause other required packages to be not found anymore. Hence prepend it. See #292
+---
+diff --git a/qcengine-0.26.0.orig/qcengine/programs/psi4.py b/qcengine-0.26.0/qcengine/programs/psi4.py
+index 7dd4d5e..437cdea 100644
+--- a/qcengine-0.26.0.orig/qcengine/programs/psi4.py
+++ b/qcengine-0.26.0/qcengine/programs/psi4.py
+@@ -66,7 +66,9 @@ class Psi4Harness(ProgramHarness):
+         if psiapi and not psithon:
+             psiimport = str(Path(which_import("psi4")).parent.parent)
+             env = os.environ.copy()
+-            env["PYTHONPATH"] = psiimport
+            pythonpath = env.get("PYTHONPATH")
+            # Prepend psiimport to $PYTHONPATH (carefull if it's empty/unset)
+            env["PYTHONPATH"] = os.pathsep.join([psiimport, pythonpath] if pythonpath else [psiimport])
+             with popen(["python", "-c", "import psi4; print(psi4.executable[:-5])"], popen_kwargs={"env": env}) as exc:
+                 exc["proc"].wait(timeout=30)
+             os.environ["PATH"] += os.pathsep + exc["stdout"].split()[-1]
--- a/s/simple-dftd3/simple-dftd3-0.7.0-foss-2021b.eb
+++ b/s/simple-dftd3/simple-dftd3-0.7.0-foss-2021b.eb
@ -0,0 +1,43 @@
+# IT4Innovations 2023
+# JK
+# J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'CMakeNinja'
+
+name = 'simple-dftd3'
+version = '0.7.0'
+
+homepage = 'https://github.com/dftd3/simple-dftd3'
+description = """A simple drop-in replacement for dftd3.
+This program provides a small and easy to use implementation of the DFT-D3 
+dispersion correction (see JCP 132, 154104 (2010) and JCC 32, 1456 (2011) 
+for details).
+It is mostly based on the dftd4 program and borrows one or two ideas from 
+the implementation in ased3."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = ['https://github.com/dftd3/simple-dftd3/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['19400a176eb4dcee7b89181a5a5f0033fe6b05c52821e54896a98448761d003a']
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+    ('Ninja', '1.10.2'),
+]
+
+dependencies = [
+    ('TOML-Fortran', '0.3.1'),
+    ('mctc-lib', '0.3.1'),
+    ('mstore', '0.2.0'),
+]
+
+test_cmd = 'ctest'
+runtest = ''
+
+sanity_check_paths = {
+    'files': ['bin/s-dftd3', 'lib/libs-dftd3.a'],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'lib'